rs2927488

Variant names:

• chr19-44728212-G-A
• rs2927488

Your query was ambiguous. Multiple possible variants found:

• chr19-44728212-G-A
• chr19-44728212-G-C
• chr19-44728212-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.225 in 152,092 control chromosomes in the GnomAD database, including 4,036 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.22 (4036 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.35

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34174 AN: 151974 Hom.: 4032 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.247

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.225 AC: 34184 AN: 152092 Hom.: 4036 Cov.: 32 AF XY: 0.225 AC XY: 16697 AN XY: 74346

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.234

Gnomad4 ASJ AF: 0.345

Gnomad4 EAS AF: 0.160

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.206

Gnomad4 NFE AF: 0.238

Gnomad4 OTH AF: 0.246

Alfa AF: 0.240 Hom.: 9266

Bravo AF: 0.225

Asia WGS AF: 0.251 AC: 875 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.0
DANN	Benign	0.78

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2927488; hg19: chr19-45231478;